Browsing by Author "Anshika Srivastava"

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Correction to: Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations (Scientific Reports, (2024), 14, 1, (7822), 10.1038/s41598-024-54607-7)
(Nature Research, 2024) Rudra Kumar Pandey; Anshika Srivastava; Rahul Kumar Mishra; Prajjval Pratap Singh; Gyaneshwer Chaubey
Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-024-54607-7, published online 03 April 2024 The original version of this Article contained errors in the Material and Methods section and in the legend of Figure 3 (A, B, C). In the Material and Methods section, under the subheading ‘Insilco analysis’, “To analyse the TMPRSS2 expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.” now reads: “To analyse the FURIN expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.” In the legend of Figure 3, “(A) and (B) display the allele frequency distribution of rs2070788 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.” now reads: “(A) and (B) display the allele frequency distribution of rs1981458 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.” “The linear regression graph depicts the association between the rs1981458 allele frequency of the TMPRSS2 gene with COVID-19 CFR.” now reads: “The linear regression graph depicts the association between the rs1981458 allele frequency of the FURIN gene with COVID-19 CFR.” The original Article has been corrected. © The Author(s) 2024.
Genetic and linguistic non-correspondence suggests evidence for collective social climbing in the Kol tribe of South Asia
(Nature Research, 2020) Anshika Srivastava; Prajjval Pratap Singh; Audditiya Bandopadhyay; Pooja Singh; Debashruti Das; Rakesh Tamang; Akhilesh Kumar Chaubey; Pankaj Shrivastava; George van Driem; Gyaneshwer Chaubey
Both classical and recent genetic studies have unanimously concluded that the genetic landscape of South Asia is unique. At long distances the ‘isolation-by-distance’ model appears to correspond well with the genetic data, whereas at short distances several other factors, including the caste, have been shown to be strong determinant factors. In addition with these, tribal populations speaking various languages add yet another layer of genetic complexity. The Kol are the third most populous tribal population in India, comprising communities speaking Austroasiatic languages of the Northern Munda branch. Yet, the Kol have not hitherto undergone in-depth genetic analysis. In the present study, we have analysed two Kol groups of central and western India for hundreds thousands of autosomal and several mitochondrial DNA makers to infer their fine genetic structure and affinities to other Eurasian populations. In contrast, with their known linguistic affinity, the Kol share their more recent common ancestry with the Indo-European and Dravidian speaking populations. The geographic-genetic neighbour tests at both the temporal and spatial levels have suggested some degree of excess allele sharing of Kol1 with Kol2, thereby indicating their common stock. Our extensive analysis on the Kol ethnic group shows South Asia to be a living genetics lab, where real-time tests can be performed on existing hypotheses. © 2020, The Author(s).
Genetic Association of ACE2 rs2285666 Polymorphism With COVID-19 Spatial Distribution in India
(Frontiers Media S.A., 2020) Anshika Srivastava; Audditiya Bandopadhyay; Debashurti Das; Rudra Kumar Pandey; Vanya Singh; Nargis Khanam; Nikhil Srivastava; Prajjval Pratap Singh; Pavan Kumar Dubey; Abhishek Pathak; Pranav Gupta; Niraj Rai; Gazi Nurun Nahar Sultana; Gyaneshwer Chaubey
Studies on host-pathogen interaction have identified human ACE2 as a host cell receptor responsible for mediating infection by coronavirus (COVID-19). Subsequent studies have shown striking difference of allele frequency among Europeans and Asians for a polymorphism rs2285666, present in ACE2. It has been revealed that the alternate allele (TT-plus strand or AA-minus strand) of rs2285666 elevate the expression level of this gene upto 50%, hence may play a significant role in SARS-CoV-2 susceptibility. Therefore, we have first looked the phylogenetic structure of rs2285666 derived haplotypes in worldwide populations and compared the spatial frequency of this particular allele with respect to the COVID-19 infection as well as case-fatality rate in India. For the first time, we ascertained a significant positive correlation for alternate allele (T or A) of rs2285666, with the lower infection as well as case-fatality rate among Indian populations. We trust that this information will be useful to understand the role of ACE2 in COVID-19 susceptibility. © Copyright © 2020 Srivastava, Bandopadhyay, Das, Pandey, Singh, Khanam, Srivastava, Singh, Dubey, Pathak, Gupta, Rai, Sultana and Chaubey.
Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 case fatality rate among Indian populations
(Elsevier B.V., 2022) Rudra Kumar Pandey; Anshika Srivastava; Prajjval Pratap Singh; Gyaneshwer Chaubey
SARS-CoV-2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the disparity in disease susceptibility between populations. Therefore, in the present study, we have used next-generation sequencing (NGS) data of world populations from 393 individuals and analyzed the TMPRSS2 gene using a haplotype-based approach with a major focus on South Asia to study its phylogenetic structure and their haplotype sharing among various populations worldwide. Our analysis of phylogenetic relatedness showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on the ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. Considering the significance of the TMPRSS2 gene in the SARS-CoV-2 pathogenicity, COVID-19 infection and intensity trends could be directly associated with increased expression therefore, we have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate (CFR). Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the CFR among Indian populations. Further our cis eQTL analysis of rs2070788 shows that the GG genotype of the rs2070788 tends to have a significantly higher expression of TMPRSS2 gene in the lung compared to the AG and AA genotypes thus validating the previous observation and therefore it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in understanding the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk. © 2022
Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Alpha Variant in India
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Jahnavi Parasar; Rudra Kumar Pandey; Yashvant Patel; Prajjval Pratap Singh; Anshika Srivastava; Rahul Kumar Mishra; Bhupendra Kumar; Niraj Rai; Vijaya Nath Mishra; Pankaj Shrivastava; P. B. Kavi Kishor; Prashanth Suravajhala; Rakesh Tamang; Ajai Kumar Pathak; Gyaneshwer Chaubey
After the spill to humans, in the evolutionary timeline of SARS-CoV-2, several positively selected variants have emerged. A phylogeographic study on these variants can reveal their spatial and temporal distribution. In December 2020, the alpha variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which has been designated as a variant of concern (VOC) by the WHO, was discovered in the south-eastern United Kingdom (UK). Slowly, it expanded across India, with a considerable number of cases, particularly in North India. This study focuses on determining the prevalence and expansion of the Alpha variants in various parts of India mainly by using phylospatial analysis. The genetic diversity estimation has helped us to understand various evolutionary forces that have shaped the spatial distribution of this variant during its peak. Overall, our study paves the way to understanding the evolution and expansion of a virus variant, which may help to mitigate in the case of any future wave. © 2023 by the authors.
Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations
(Springer, 2019) Ajai K Pathak; Anshika Srivastava; Prajjval Pratap Singh; Debashruti Das; Audditiya Bandopadhyay; Pooja Singh; Gyaneshwer Chaubey
The South Asian populations have a mosaic of ancestries likely due to the interactions of long-term populations of the landmass and those of East and West Eurasia. Apart from prehistoric dispersals, there are some known population movements to India. In this study, we focussed on the migration of Jewish and Parsi populations on temporal and spatial scales. The existence of Jewish and Parsi communities in India are recorded since ancient times. However, due to the lack of high-resolution genetic data, their origin and affiliation with other Indian and non-Indian populations remains shrouded in legends. Earlier genetic studies on populations of Indian Jews have found evidence for a minor shared ancestry of Indian Jews with Middle Eastern (Jews) populations, whereas for Parsis, the Iranian link was proposed. Recently, in our high-resolution study, we were able to quantify the admixture dynamics of these groups, which has suggested a male-biased admixture. Here, we added the newly available ancient samples and revisited the interplay of genes and cultures. Thus, in this study we reconstructed a broad genetic profile of Indian Jews and Parsis to paint a fine-grained picture of these ethnic groups. © 2019, Indian Academy of Sciences.
Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations
(Public Library of Science, 2020) Anshika Srivastava; Rudra Kumar Pandey; Prajjval Pratap Singh; Pramod Kumar; Avinash Arvind Rasalkar; Rakesh Tamang; George van Driem; Pankaj Shrivastava; Gyaneshwer Chaubey
It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans. Copyright: © 2020 Srivastava et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations
(Nature Research, 2024) Rudra Kumar Pandey; Anshika Srivastava; Rahul Kumar Mishra; Prajjval Pratap Singh; Gyaneshwer Chaubey
SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, it enters the host cell by activating the ACE2 receptor with the help of two proteasesi.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Previous studies have shown that the role of ACE2 and TMPRSS2 gene variants in understanding COVID-19 susceptibility among Indian populations. Nevertheless, a knowledge gap exists concerning the COVID-19 susceptibility of Furin gene variants among diverse South Asian ethnic groups. Investigating the role of Furin gene variants and their global phylogeographic structure is essential to comprehensively understanding COVID-19 susceptibility in these populations. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's with COVID-19 Case Fatality Rate (CFR) that could be epidemiologically associated with disease severity outcomes. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its Phylogeographic structure among diverse world populations. We found a significant positive association for the SNP rs1981458 with COVID-19 CFR (p < 0.05) among diverse Indian populations at different timelines of the first and second waves. Further, QTL and other regulatory analyses showed various significant associations for positive regulatory roles of rs1981458 and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein–protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogeographic architecture of the Furin gene demonstrated a closer genetic affinity of South Asia with West Eurasian populations. Therefore, it is worth proposing that for the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, with the collective information from these three important genes (ACE2, TMPRSS2 and Furin) we modelled COVID-19 susceptibilityof South Asia in between these two major ancestries with an inclination towards West Eurasia. In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential.This study also highlights that the genetic structure for COVID-19 susceptibilityof South Asia is distinct, however, inclined to the West Eurasian population. We believe this insight may be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic. © The Author(s) 2024.
Publisher Correction: The major genetic risk factor for severe COVID‑19 does not show any association among South Asian populations (Scientific Reports, (2021), 11, 1, (12346), 10.1038/s41598-021-91711-4)
(Nature Research, 2021) Prajjval Pratap Singh; Anshika Srivastava; Gazi Nurun Nahar Sultana; Nargis Khanam; Abhishek Pathak; Prashanth Suravajhala; Royana Singh; Pankaj Shrivastava; George van Driem; Kumarasamy Thangaraj; Gyaneshwer Chaubey
In the original version of this Article, Kumarasamy Thangaraj was omitted as a corresponding author. Correspondence and request for materials should also be addressed to thangs@ccmb.res.in. In addition, the email address of the co-corresponding author Gyaneshwer Chaubey was incorrectly given as thangs@ccmb.res.in. Correspondence and request for materials should also be addressed to gyaneshwer.chaubey@bhu.ac.in. The original Article has been corrected. © 2021, The Author(s).
Studying C-reactive protein and D-dimer levels in blood may prevent severe complications: A study in Bangladeshi COVID-19 patients
(Frontiers Media S.A., 2022) Gazi Nurun Nahar Sultana; Anshika Srivastava; Khalida Akhtaar; Prajjval Pratap Singh; Md. Anarul Islam; Rahul Kumar Mishra; Gyaneshwer Chaubey
The ongoing COVID-19 pandemic has been a scientific, medical and social challenge. Since clinical course of this disease is largely unpredictable and can develop rapidly causing severe complications, it is important to identify laboratory biomarkers, which may help to classify patient’s severity during initial stage. Previous studies have suggested C—reactive protein (inflammatory) and D-dimer (biochemical) as an effective biomarker. The differential severity in patients across the world and our limited understanding in the progression of the disease calls for a multi-country analysis for biomarkers. Therefore, we have analyzed these biomarkers among 228 Bangladeshi COVID-19 patients. We observed significant association of COVID-19 severity with these two biomarkers. Thus, we suggest to use these biomarkers for Bangladeshi COVID-19 patients for better disease monitoring. Such validated preventive measures may decrease the case fatality ratio substantially. Copyright © 2022 Sultana, Srivastava, Akhtaar, Singh, Islam, Mishra and Chaubey.
The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations
(Nature Research, 2021) Prajjval Pratap Singh; Anshika Srivastava; Gazi Nurun Nahar Sultana; Nargis Khanam; Abhishek Pathak; Prashanth Suravajhala; Royana Singh; Pankaj Shrivastava; George van Driem; Kumarasamy Thangaraj; Gyaneshwer Chaubey
With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India. © 2021, The Author(s).
The peopling of Lakshadweep Archipelago
(Nature Publishing Group, 2019) Mohammed S. Mustak; Niraj Rai; Mohan Rao Naveen; Satya Prakash; S. Justin Carlus; Nagarjuna Pasupuleti; Anshika Srivastava; Prajjval Pratap Singh; Idrees Babu; Pavan Kumar Dubey; Gyaneshwer Chaubey; Kumarasamy Thangaraj
The archipelago of Lakshadweep is considered as a stopover to the maritime route since ancient time. It is not very clear when the human first occupied these islands, however in the long history of the islands, the local legends suggest that Lakshadweep has been ruled by different kingdoms. To have a better understanding of peopling of Lakshadweep, we have analysed 557 individuals from eight major islands for mitochondrial DNA and 166 individuals for Y chromosome markers. We found a strong founder effect for both paternal and maternal lineages. Moreover, we report a close genetic link of Lakshadweep islanders with the Maldives, Sri Lanka and India. Most of the Lakshadweep islands share the haplogroups specific to South Asia and West Eurasia, except Minicoy Island that also shares haplogroups of East Eurasia. The paternal and maternal ancestries of the majority of island populations suggest their arrival from distinct sources. We found that the maternal ancestry was closer to South Indian populations, whereas the paternal ancestry was overwhelmed with the haplogroups, more common in the Maldives and North of India. In conclusion, our first genetic data suggest that the majority of human ancestry in Lakshadweep is largely derived from South Asia with minor influences from East and West Eurasia. © 2019, The Author(s).